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ratschlab / spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
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IndexError at Event Calling #97

Closed J0bbie closed 2 years ago

J0bbie commented 5 years ago

Description

Dear Andre,

Whilst following the step-wise procedure for use on large cohorts, SplAdder returns an error on the last step (4. Event Calling).

All previous steps ran just fine and prior to the final error, it creates the individual pickles for the given event-types: merge_graphs_intron_retention_C3.pickle, merge_graphs_intron_retention_C3.pickle, merge_graphs_alt_5prime_C3.pickle, etc.

Any idea what could be the issue? If I need to provide some more information, feel free to ask! Thanks!

What I Did

# Generate splicing graph per sample, in parallel to speed things up.
for BAM in  *sorted*_markDup.bam
do echo "/usr/local/bin/spladder build -o <output>/ -b ${BAM} -a gencode.v30.annotation.gtf --merge-strat single --no-extract-ase --parallel 10 -v --primary-only";
done

# Merge the graphs
/usr/local/bin/spladder build -o <output>/ -a gencode.v30.annotation.gtf -b <26 BAM files> --merge-strat merge_graphs --no-extract-ase -v

# Quantify per sample
for BAM in  *sorted*_markDup.bam
do echo "/usr/local/bin/spladder build -o <output>/ -b ${BAM} -a gencode.v30.annotation.gtf --merge-strat merge_graphs --no-extract-ase --quantify-graph --qmode single -v"
done

# Merge the quantification.
/usr/local/bin/spladder build -o <output>/ -a gencode.v30.annotation.gtf -b <26 BAM files> --merge-strat merge_graphs --no-extract-ase --quantify-graph --qmode collect -v

# Call the events. (Gives error)
/usr/local/bin/spladder build -o <output>/ -a gencode.v30.annotation.gtf -b <26 BAM files> --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skips --verbose

Traceback

confidence 3 / sample 0
Loading gene structure from <output>/spladder/genes_graph_conf3.merge_graphs.pickle ...
... done.
<output>/merge_graphs_intron_retention_C3.pickle already exists
<output>/merge_graphs_exon_skip_C3.pickle already exists
<output>/merge_graphs_alt_5prime_C3.pickle and <output>/merge_graphs_alt_3prime_C3.pickle already exists
<output>/merge_graphs_mutex_exons_C3.pickle already exists
<output>/merge_graphs_intron_retention_C3.pickle already exists
<output>/merge_graphs_exon_skip_C3.pickle already exists
<output>/merge_graphs_alt_5prime_C3.pickle already exists
<output>/merge_graphs_alt_3prime_C3.pickle already exists
<output>/merge_graphs_mutex_exons_C3.pickle already exists
analyzing events with confidence 3
.Traceback (most recent call last):
  File "/usr/local/bin/spladder", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/dist-packages/spladder/spladder.py", line 195, in main
    options.func(options)
  File "/usr/local/lib/python3.6/dist-packages/spladder/spladder_build.py", line 253, in spladder
    analyze_events(options, options.event_types[e_idx])
  File "/usr/local/lib/python3.6/dist-packages/spladder/alt_splice/analyze.py", line 104, in analyze_events
    (events_all, counts) = verify_all_events(events_all, sp.arange(len(options.strains)), options.bam_fnames, event_type, options)
  File "/usr/local/lib/python3.6/dist-packages/spladder/alt_splice/verify.py", line 493, in verify_all_events
    segments = sp.atleast_2d(IN['segments'][gr_idx_segs, :])[:, strain_idx]
IndexError: index 1 is out of bounds for axis 1 with size 1
akahles commented 5 years ago

Dear @J0bbie,

Thanks for reporting. At a first glance, I don't see anything obviously wrong with your calls. From the error message I can get that the counts have the wrong dimensions. I will try to reproduce this on my end and come back to you once I know more.

Just as a hint, could you send me the dimensions of the count arrays. You can get them from:

h5ls -r <output>/spladder/genes_graph_conf3.merge_graphs.count.hdf5

Thanks, Andre

J0bbie commented 5 years ago

Dear Andre,

Thanks for the quick response! Here's the output:

h5ls -r spladder/genes_graph_conf3.merge_graphs.count.hdf5
/                        Group
/edge_idx                Dataset {398841}
/edges                   Dataset {398841, 26/Inf}
/gene_ids_edges          Dataset {398841, 1}
/gene_ids_segs           Dataset {661774, 1}
/gene_names              Dataset {58870, 1}
/seg_len                 Dataset {661774, 1}
/seg_pos                 Dataset {661774, 1}
/segments                Dataset {661774, 1}
/strains                 Dataset {26/Inf}

Thanks,

Job

akahles commented 5 years ago

Ah, this is very helpful. It looks like the collection step did not work as expected. For instance, the line

/segments                Dataset {661774, 1}

should be 

/segments                Dataset {661774, 26}

This gives me something to search for. Will post here what I find.

jfass commented 5 years ago

Seeing the same thing here:

$ spladder build -o spladder_out.chr9 -a gencode.v19.annotation.pc.chr9.gtf -b $allbams --parallel 2 -c 0 --set-mm-tag nM --readlen 150

confidence 0 / sample 0
Loading gene structure from spladder_out.chr9/spladder/genes_graph_conf0.merge_graphs.pickle ...
... done.
spladder_out.chr9/merge_graphs_intron_retention_C0.pickle already exists
spladder_out.chr9/merge_graphs_exon_skip_C0.pickle already exists
spladder_out.chr9/merge_graphs_alt_5prime_C0.pickle and spladder_out.chr9/merge_graphs_alt_3prime_C0.pickle already exists
spladder_out.chr9/merge_graphs_mult_exon_skip_C0.pickle already exists
spladder_out.chr9/merge_graphs_mutex_exons_C0.pickle already exists
spladder_out.chr9/merge_graphs_intron_retention_C0.pickle already exists
spladder_out.chr9/merge_graphs_exon_skip_C0.pickle already exists
spladder_out.chr9/merge_graphs_mult_exon_skip_C0.pickle already exists
spladder_out.chr9/merge_graphs_alt_5prime_C0.pickle already exists
spladder_out.chr9/merge_graphs_alt_3prime_C0.pickle already exists
spladder_out.chr9/merge_graphs_mutex_exons_C0.pickle already exists
analyzing events with confidence 0
.Traceback (most recent call last):
  File "/home/ubuntu/spladder/spladder-venv/bin/spladder", line 10, in <module>
    sys.exit(main())
  File "/home/ubuntu/spladder/spladder-venv/lib/python3.5/site-packages/spladder/spladder.py", line 192, in main
    options.func(options)
  File "/home/ubuntu/spladder/spladder-venv/lib/python3.5/site-packages/spladder/spladder_build.py", line 253, in spladder
    analyze_events(options, options.event_types[e_idx])
  File "/home/ubuntu/spladder/spladder-venv/lib/python3.5/site-packages/spladder/alt_splice/analyze.py", line 104, in analyze_events
    (events_all, counts) = verify_all_events(events_all, sp.arange(len(options.strains)), options.bam_fnames, event_type, options)
  File "/home/ubuntu/spladder/spladder-venv/lib/python3.5/site-packages/spladder/alt_splice/verify.py", line 493, in verify_all_events
    segments = sp.atleast_2d(IN['segments'][gr_idx_segs, :])[:, strain_idx]
IndexError: index 1 is out of bounds for axis 1 with size 1

$ h5ls -r spladder_out.chr9/spladder/genes_graph_conf0.merge_graphs.count.hdf5                                                                                                                                                                                          
/                        Group
/edge_idx                Dataset {35428}
/edges                   Dataset {35428, 32/Inf}
/gene_ids_edges          Dataset {35428, 1}
/gene_ids_segs           Dataset {38150, 1}
/gene_names              Dataset {808, 1}
/seg_len                 Dataset {38150, 1}
/seg_pos                 Dataset {38150, 1}
/segments                Dataset {38150, 1}
/strains                 Dataset {32/Inf}
akahles commented 5 years ago

This should be fixed both in master and development. Will add it to the next release.

jfass commented 5 years ago

Hi Andre, I cloned and built the repo (and I'm seeing the 2.2.3 tag), and now I'm getting:

$ cat chr6.eventCalling.err
Traceback (most recent call last):
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/bin/spladder", line 11, in <module>
    load_entry_point('spladder==2.2.3', 'console_scripts', 'spladder')()
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 542, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2569, in load_entry_point
    return ep.load()
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2229, in load
    return self.resolve()
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2235, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/spladder-2.2.3-py3.5.egg/spladder/spladder.py", line 10, in <module>
    from .spladder_test import spladder_test
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/spladder-2.2.3-py3.5.egg/spladder/spladder_test.py", line 3, in <module>
    import statsmodels.api as sm
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/api.py", line 3, in <module>
    from . import iolib
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/iolib/__init__.py", line 1, in <module>
    from .foreign import StataReader, genfromdta, savetxt
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/iolib/foreign.py", line 14, in <module>
    from statsmodels.compat.python import (zip, lzip, lmap, lrange, string_types, long, lfilter,
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/compat/__init__.py", line 1, in <module>
    from statsmodels.tools._testing import PytestTester
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/tools/__init__.py", line 1, in <module>
    from .tools import add_constant, categorical
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/statsmodels-0.10.1-py3.5-linux-x86_64.egg/statsmodels/tools/tools.py", line 7, in <module>
    import pandas as pd
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/__init__.py", line 55, in <module>
    from pandas.core.api import (
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/api.py", line 5, in <module>
    from pandas.core.arrays.integer import (
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/arrays/__init__.py", line 1, in <module>
    from .array_ import array  # noqa: F401
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/arrays/array_.py", line 7, in <module>
    from pandas.core.dtypes.common import (
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/dtypes/common.py", line 11, in <module>
    from pandas.core.dtypes.dtypes import (
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/dtypes/dtypes.py", line 53, in <module>
    class Registry:
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/site-packages/pandas-0.25.1-py3.5-linux-x86_64.egg/pandas/core/dtypes/dtypes.py", line 84, in Registry
    self, dtype: Union[Type[ExtensionDtype], str]
  File "/usr/lib/python3.5/typing.py", line 552, in __getitem__
    dict(self.__dict__), parameters, _root=True)
  File "/usr/lib/python3.5/typing.py", line 512, in __new__
    for t2 in all_params - {t1} if not isinstance(t2, TypeVar)):
  File "/usr/lib/python3.5/typing.py", line 512, in <genexpr>
    for t2 in all_params - {t1} if not isinstance(t2, TypeVar)):
  File "/usr/lib/python3.5/typing.py", line 1077, in __subclasscheck__
    if super().__subclasscheck__(cls):
  File "/home/ubuntu/spladder/spladder-2.2.3-venv/lib/python3.5/abc.py", line 225, in __subclasscheck__
    for scls in cls.__subclasses__():
TypeError: descriptor '__subclasses__' of 'type' object needs an argument

From the last step:

cat chrList.txt | while read chr; do
  spladder build -o spladder_out.${chr} -a gencode.v19.annotation.pc.${chr}.gtf \
    -b $allbams --parallel 2 -c 0 --set-mm-tag nM --readlen 150 \
    --event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skips \
    --verbose 2>${chr}.eventCalling.err 1>${chr}.eventCalling.out &
done

Any thoughts?

~Joe

akahles commented 5 years ago

Hi Joe,

this seems unrelated to the previous issue. Would you mind opening a new one? Otherwise it is hard to track for me what has been worked on and what it still open.

Does this happen on a fresh installation? It looks to me as if the environment has some issues when loading statsmodels.

Cheers,

Andre

jfass commented 5 years ago

Hey Andre,

Not sure if this is the same error ... but the traceback is similar. I'm having no problems with the initial build on most chromosomes, but seeing problems on (hg19) chr3, 5, etc ... a handful. While the successful initial build steps with "--sparse-bam" generate both a "alignments.conf_3.filt.hdf5" and a "alignments.hdf5" file, I'm seeing only the "alignments.conf_3.filt.hdf5" file for the times when the step errors out. The traceback is:

Traceback (most recent call last):
  File "/home/ubuntu/SplAdder/spladder-venv/bin/spladder", line 10, in <module>
    sys.exit(main())
  File "/home/ubuntu/SplAdder/spladder-venv/lib/python3.5/site-packages/spladder/spladder.py", line 188, in main
    options.func(options)
  File "/home/ubuntu/SplAdder/spladder-venv/lib/python3.5/site-packages/spladder/spladder_build.py", line 152, in spladder
    spladder_core(options)
  File "/home/ubuntu/SplAdder/spladder-venv/lib/python3.5/site-packages/spladder/core/spladdercore.py", line 21, in spladder_core
    genes = gen_graphs(genes, options)
  File "/home/ubuntu/SplAdder/spladder-venv/lib/python3.5/site-packages/spladder/core/gen_graphs.py", line 118, in gen_graphs
    genes, inserted_ = insert_intron_retentions(genes, options)
  File "/home/ubuntu/SplAdder/spladder-venv/lib/python3.5/site-packages/spladder/editgraph.py", line 324, in insert_intron_retentions
    exon_coverage[k] = sp.median(sp.sum(tracks[:, idx], axis=0).astype('float')) # median coverage for exon k
IndexError: index 70609 is out of bounds for axis 1 with size 16138

For the failing cases, here's the "alignments.conf_3.filt.hdf5" file listing:

$ h5ls -r ~/data/dedups/1610213826.dedup.conf_3.filt.hdf5                                                                                                                                                                                                                                                                    
/                        Group
/chr20_introns_m         Dataset {0, 3}
/chr20_introns_p         Dataset {25, 3}
/chr20_reads_col         Dataset {1556008}
/chr20_reads_dat         Dataset {1556008}
/chr20_reads_row         Dataset {1556008}
/chr20_reads_shp         Dataset {2}

... for the successful cases, here's the "alignments.conf_3.filt.hdf5" file:

$ h5ls -r ~/data/dedups/spladder.sparsebams.chr2/1610213826.dedup.conf_3.filt.hdf5                                                                                                                                                                                                                                           
/                        Group
/chr2_introns_m          Dataset {0, 3}
/chr2_introns_p          Dataset {72, 3}
/chr2_reads_col          Dataset {4335159}
/chr2_reads_dat          Dataset {4335159}
/chr2_reads_row          Dataset {4335159}
/chr2_reads_shp          Dataset {2}

... and the "alignments.hdf5" files:

$ h5ls -r ~/data/dedups/spladder.sparsebams.chr2/1610213826.dedup.hdf5 
/                        Group
/chr2_introns_m          Dataset {0, 3}
/chr2_introns_p          Dataset {16240, 3}
/chr2_reads_col          Dataset {6306090}
/chr2_reads_dat          Dataset {6306090}
/chr2_reads_row          Dataset {6306090}
/chr2_reads_shp          Dataset {2}

~Joe

akahles commented 5 years ago

This looks like some problem with creating the sparse bams. I am re-opening the issue to keep track. Will try to have a look soon.

jfass commented 5 years ago

Awesome- thanks Andre ... lmk if you could use any example files / hdf5 dumps, etc.

tarjand commented 4 years ago

Hi @akahles,

I might have a similar error that appears unresolved in version 2.4.2

I ran all the steps as outlined in your large cohorts guide for 128 samples. Everything seems to work until the event calling step. Event calling is failing.

I noticed in my genes_graph_conf2.merge_graphs.count.hdf5 file the /segments Dataset size format is different than what you show above - it ends with /Inf

I get similar errors for other event types or if I run without the parallel option.

Thanks for any insight you can share! Really appreciate your help.

-Dan

merge_graphs.count.hdf5 overview

 h5ls -r genes_graph_conf2.merge_graphs.count.hdf5
/                        Group
/edge_idx                Dataset {906328}
/edges                   Dataset {906328, 128/Inf}
/gene_ids_edges          Dataset {906328, 1}
/gene_ids_segs           Dataset {1093862, 1}
/gene_names              Dataset {57820, 1}
/seg_len                 Dataset {1093862, 1}
/seg_pos                 Dataset {1093862, 128/Inf}
/segments                Dataset {1093862, 128/Inf}
/strains                 Dataset {128/Inf}

Command

spladder build \
  --outdir spladder_out \
  --parallel 2 \
  --annotation ${annotation_spladder} \
  --bams ${bamfiles} \
  --verbose \
  --confidence ${confidence} \
  --event-types exon_skip

Traceback

Loading gene structure from spladder_out/spladder/genes_graph_conf2.merge_graphs.pickle ...
... done.
spladder_out/merge_graphs_exon_skip_C2.pickle already exists
spladder_out/merge_graphs_exon_skip_C2.pickle already exists
analyzing events with confidence 2
./usr/local/lib/python3.5/dist-packages/spladder/alt_splice/verify.py:201: RuntimeWarning: invalid value encountered in double_scalars
  info[2] = sp.sum(counts_segments[seg_exon_pre] * seg_lens[seg_exon_pre]) /sp.sum(seg_lens[seg_exon_pre])
/usr/local/lib/python3.5/dist-packages/spladder/alt_splice/verify.py:203: RuntimeWarning: invalid value encountered in double_scalars
  info[3] = sp.sum(counts_segments[seg_exon_aft] * seg_lens[seg_exon_aft]) /sp.sum(seg_lens[seg_exon_aft])
/usr/local/lib/python3.5/dist-packages/spladder/alt_splice/verify.py:205: RuntimeWarning: invalid value encountered in double_scalars
  info[1] = sp.sum(counts_segments[seg_exon] * seg_lens[seg_exon]) /sp.sum(seg_lens[seg_exon])
Traceback (most recent call last):
  File "/usr/local/bin/spladder", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.5/dist-packages/spladder/spladder.py", line 190, in main
    options.func(options)
  File "/usr/local/lib/python3.5/dist-packages/spladder/spladder_build.py", line 259, in spladder
    analyze_events(options, options.event_types[e_idx])
  File "/usr/local/lib/python3.5/dist-packages/spladder/alt_splice/analyze.py", line 104, in analyze_events
    (events_all, counts) = verify_all_events(events_all, sp.arange(len(options.strains)), options.bam_fnames, event_type, options)
  File "/usr/local/lib/python3.5/dist-packages/spladder/alt_splice/verify.py", line 504, in verify_all_events
    ver, info = verify_exon_skip(ev[i], genes[g_idx], segments[:, s_idx].T,  sp.c_[curr_edge_idx, edges[:, s_idx]], options)
  File "/usr/local/lib/python3.5/dist-packages/spladder/alt_splice/verify.py", line 214, in verify_exon_skip
    idx = sp.where(counts_edges[:, 0] == sp.ravel_multi_index([seg_exon_pre[-1], seg_exon[0]], segs.seg_edges.shape))[0]
IndexError: index -1 is out of bounds for axis 0 with size 0

versions

root@091238ad2e40:~# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.1 LTS
Release:    16.04
Codename:   xenial

root@091238ad2e40:~# python3 --version
Python 3.5.2

root@091238ad2e40:~# pip3 list | grep spladder
spladder            2.4.2
gtollefson commented 3 years ago

@tarjand I'm experiencing the same issue. Were you ever able to resolve it?

akahles commented 2 years ago

This should be resolved with the latest release. Please re-open if still an issue.

stasrira commented 6 months ago

Hello Andre, I am using spladder==3.0.4, python=3.8.15 and having an issue similar to the one discussed here. All steps up to the event calling went fine. However, this step produced an error. So far, all events generated the same error.

Here is the command (exon_skip here used as an example): spladder build -v --parallel 2 -o /path/to/hg38_gencode_v30/genome.gtf -b /path/to/spladder/alignments.txt --event-types exon_skip

Here is the content of the log file. I am including just the bottom part of it.

[################################################# ] 7912 / 7913 (100%) - took 13 sec (ETA: 0 sec)
[##################################################] 7913 / 7913 (100%) - took 13 sec (ETA: 0 sec)
[##################################################] 7914 / 7913 (100%) - took 13 sec (ETA: 0 sec)

Remove 0-length intron events

Make exon_skip events unique by event
. . . . . . . . . . 10000
. . . . . . . . . . 20000
. . . . . . . . . . 30000
. . . . . . . . . . 40000
. . . . . . . . . . 50000
. . . . . . . . . . 60000
. . . . . . . . . . 70000
. . . . . . . . . . 80000
. . . . . . . . . . 90000
. . . . . . . . . . 100000
. . . . . . . . . . 110000
. . . . . . . . . . 120000
. . . . . . . . . . 130000
. . . . . . . . . . 140000
. . . . . . . . . . 150000
. . . . . . . . . . 160000
. . . . . . . . . . 170000
. . . . . . . . . . 180000
. . . . . . . . . . 190000
. . . . . . . . . . 200000
. . . . . . . . . . 210000
events dropped: 144309
saving exon skips to /sc/arion/projects/sealfs01a/german/projects/ECHO/JH-LymeRNAseq_206_157_1_SR1/spladder/merge_graphs_exon_skip_C3.pickle
analyzing events with confidence 3
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/site-packages/spladder/alt_splice/verify.py", line 504, in verify_wrapper
    segments = np.atleast_2d(IN['segments'][gr_idx_segs, :])[:, sample_idx]
IndexError: index 10 is out of bounds for axis 1 with size 10
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/bin/spladder", line 8, in <module>
    sys.exit(main())
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/site-packages/spladder/spladder.py", line 229, in main
    options.func(options)
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/site-packages/spladder/spladder_build.py", line 163, in spladder
    analyze_events(event_type, options.bam_fnames, options)
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/site-packages/spladder/alt_splice/analyze.py", line 95, in analyze_events
    (events_all, counts, verified) = verify_all_events(events_all, np.arange(len(options.samples)), bam_fnames, event_type, options)
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/site-packages/spladder/alt_splice/verify.py", line 590, in verify_all_events
    tmp = result.pop(0).get()
  File "/sc/arion/projects/sealfs01a/stas/conda/local_envs/snakemake3_mamba6a/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
IndexError: index 10 is out of bounds for axis 1 with size 10

Also, as was requested in some of the previous posts, here is the output of the h5ls -r <output>/spladder/genes_graph_conf3.merge_graphs.count.hdf5

/edge_idx                Dataset {442044}
/edges                   Dataset {442044, 10/Inf}
/gene_ids_edges          Dataset {442044, 1}
/gene_ids_segs           Dataset {691749, 1}
/gene_names              Dataset {58929, 1}
/samples                 Dataset {10/Inf}
/seg_len                 Dataset {691749, 1}
/seg_pos                 Dataset {691749, 10/Inf}
/segments                Dataset {691749, 10/Inf}